Avengers had just enough substance on it to keep it from devolving into a mindless Bay-spectacle, but let's not pretend as if it was some shining example of how to do superhero characterisation on the big-screen, because it wasn't. TDK, Iron Man, Spiderman 2 and X-Men First Class are all superior to the Avengers in that department.
Avengers has "great characterisation" in the sense that whatever it does have is very good, but that still doesn't change the fact that it doesn't have much of it to begin with. That is not a knock or criticism of the film, because that is not what the film intended to be. The film appealed to a wide audience because first and foremost, it was "fun". A hilariously fun superhero movie at that. I laughed my ass off in my cinema, so did other movie-goers.
Yes, there were some nice character moments, no one is denying that. However RDJ grated on my nerves after a while with his "witty" banter. Some of it worked, some of it didn't. There were moments that felt cliched but that's par for the course in a movie dealing with multiple superhero characters.
Don't confuse the filmmaker's intention for your own. Your opinion is respected, but if you knew what Whedon had been capable of, he can compose deft characterisation, resonant themes and subtexts brilliantly as the next auteur. Mark my words. He's skilled in genre versatility and pathos and gives so much respect to the characters. He would have respected every single character in X-Men far better than Singer did, who didn't really understand Storm or Cyclops, for instance. I'm not knocking the latter nor am I lifting Whedon at anyone's expense, but one ought to give credit when it is due.
He is a remarkably deep storyteller, but his approach is different to other filmmakers', that is all. And that is not a bad thing.
He made TA very fun, that's veritable. But he wrote it in a way that anybody not looking for deeper texts could just have a ride, while those looking for otherwise would be greatly rewarded.
There is a reason why he has been maligned by Hollywood for a long time and that is because most people in the commercial vein never really understood him. Let's not forget he was a highly sought and uncredited script doctor. If you like Toy Story (which was the first animated film to be nominated for Best Screenplay), that's because of him.
The Avengers is a popcorn flick simply because its source material was never a social commentary nor a political allegory of some sort to begin with. So to make something that is not would have not been what its fan base may have necessarily wanted, but it doesn't certainly hurt now. The source material after all was originally about diverse superheroes with big egos banding together against global threats. Nothing more, nothing less. But Whedon has translated it so well to the screen so we ought to be praising his strengths, at least more than whatever flaws he has (and he does have them, of course, but the former outweigh the latter) because we're in a unique climate for several reasons: virtually everyone who was not familiar with Whedon questioned his capacity for an ensemble film, and the fact he changed so many minds is a testament to his technical and creative ability, and secondly the solo films leading up to TA set a precedent for a new type of fllmmaking, at least for the DC, as well as in terms of box office records. It's an interesting time.